The maize genome is largely composed of retrotransposons of recent origin

Phillip John SanMiguel, Purdue University

Abstract

Detailed characterization of large segments of plant genomes has been initiated only in the last two or three years. We found at least 175 kb of retrotransposons in a 250 kb region, flanking adh1, that had previously been established as a model of the rest of the maize genome. Retrotransposons are 3–15 kb transposable elements that transpose via an RNA intermediate. Our data show that they inserted first into areas between maize genes and then into each other during successive rounds of transposition to create nested “stacks” of elements. These include 23 members of 11 retrotransposon families in this region alone. One family, the Cinful elements, was studied in some detail. Two copies of Cinful are present in the adh1 region. Both were sequenced and found to be related to a previously characterized, defective retrotransposon, Zeon1. Interestingly, while Cinful appears to lack one component of a complete retrotransposon, gag, Zeon1 possesses this component, but lacks the other: pol. I found that both possess a feature shared with a teosinte and a tobacco retrotransposon—related short tandem repeats that separate the 5′ gag or pol-containing domain from a 3′ domain of unknown function. Other retrotransposons discovered in this region, like Cinful, have copy numbers exceeding 20,000 per haploid genome but some have much lower copy numbers. Extrapolating from the retrotransposon content of the adh1 region, it was conservatively estimated that 150,000–220,000 retrotransposons compose some 50–80% of the maize genome. To ascertain when these retrotransposons inserted, the long terminal repeats (LTRs) that flank the internal domains of retrotransposons were analyzed. Generally, upon insertion, the LTRs of a retrotransposon are identical, so the mutations that accumulate over time could be used to date 17 of the insertions in the adh1 region and two from elsewhere in the maize genome. All were estimated to have inserted less than 6 million years ago and 17 of 19 within the last 3 million years.

Degree

Ph.D.

Advisors

Bennetzen, Purdue University.

Subject Area

Genetics|Molecular biology|Agronomy

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